AmpliSeq for Illumina Childhood Cancer Panel Compatible Products

Sample Information

Before preparing libraries, record information about your samples using an option available for your sequencing system:

Library Prep

Panel Description

The AmpliSeq for Illumina Childhood Cancer Panel provides a targeted resequencing solution for comprehensive evaluation of somatic variants associated with childhood and young adult cancers.

Component Number of Pools Concentration Number of Amplicons Average Amplicon Length (bp) Average Library Length (bp)
DNA 2 4X 3069 114 254
RNA 2 5X 1701 122 262
Library Prep and Index Kits

Completing the AmpliSeq for Illumina Childhood Cancer Panel protocol requires the panel and the following library prep, cDNA synthesis, and index kits. The AmpliSeq for Illumina Library PLUS Kit is available in 24-, 96-, and 384-reaction configurations.

Number of Samples

The AmpliSeq for Illumina Childhood Cancer Panel generates one DNA and one RNA library per sample. Samples can be DNA, RNA, or paired. Samples for this protocol are paired. A sample is a specimen of nucleic acid from one source, while a library is nucleic acids from a sample after preparation. A library is a unique DNA or RNA preparation that has the ends required for sequencing.

Preparing the appropriate number of samples requires the following number and combination of kits.

Number of Samples 24 Samples 96 Samples 384 Samples
Number of Libraries 48 Libraries
(24 DNA, 24 RNA)
192 Libraries
(96 DNA, 96 RNA)
768 Libraries
(384 DNA, 384 RNA)
AmpliSeq for Illumina Childhood Cancer Panel 1 4 16
AmpliSeq Library PLUS For Illumina 2 24-reaction kits 2 96-reaction kits 2 384-reaction kits
AmpliSeq CD Set A (96 reaction, 96 indexes) 1 2 8
cDNA Synthesis 1 1 4

Sequencing Guidelines

Sequence AmpliSeq for Illumina Childhood Cancer Panel libraries using the following systems and reagent kits.

System Reagent Kit Max # DNA
Samples Only per Run
Max # RNA
Samples Only per Run
Max # Combined*
Samples per Run
DNA:RNA Pooling
Volume Ratio**
Run Time
MiniSeq System MiniSeq Mid Output Reagent Kit 1 8 1 5:1 17 hours
  MiniSeq High Output Reagent Kit 5 25 4 5:1 24 hours
MiSeq System MiSeq Reagent Kit v2 3 15 2 5:1 24 hours
  MiSeq Reagent Kit v3 5 25 4 5:1 32 hours
NextSeq System NextSeq Mid Output v2 Kit 27 96 22 5:1 26 hours
  NextSeq High Output v2 Kit 83 96 48 5:1 29 hours

* Combined means paired DNA and RNA from the same sample that generates two libraries, one from each nucleic acid and separately indexed.

** Combined DNA to RNA pooling ratio based on recommended read coverage.